Ecological restoration is widely expected to rebuild biodiversity and ecosystem functioning simultaneously. Yet ecosystem functions emerge from multiple environmental controls operating across spatial and temporal scales, raising the question of whether restoring habitat structure and biological communities is sufficient to recover ecosystem functioning. We compiled 582 effect sizes from 66 studies, covering 19 biodiversity attributes and 9 ecosystem functions, to quantify how ecosystem functions responded to hydromorphological degradation and restoration and assessed whether biodiversity recovery consistently coincided with ecosystem function recovery. Functional responses varied markedly among ecosystem processes and between benchmarks (reference/ impacted), with no universal response across restoration strategies. While gross primary production and organic matter decomposition exceeded reference conditions in degraded streams and restored streams alike, nitrate uptake remained lower than in reference streams after restoration. Denitrification responses were significantly lower in restored streams relative to degraded reaches. Differences in responses between biodiversity and ecosystem functioning varied across the studied functions and did not change systematically with restoration age. Biodiversity–ecosystem functioning relationships were similarly inconsistent across functions and associated with high uncertainty. Together, our results indicate that ecosystem functioning does not recover as a single integrated property following hydromorphological restoration. Instead, individual ecosystem processes appear to recover along partially independent trajectories determined by distinct environmental controls, including nutrient supply, hydrologic exchange, organic matter dynamics, thermal regimes, and catchment-scale stressors. Functional restoration, therefore, requires more than rebuilding habitat structure and biodiversity alone: it requires restoring the environmental process domains under which ecosystem functions emerge. This shifts restoration from a paradigm centered on structural habitat recovery toward one explicitly grounded in process-based ecosystem recovery.